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Burke N, Müller G, Saggiomo V, Hassett AR, Mutterer J, Ó Súilleabháin P, Zakharov D, Healy D, Reynaud EG, Pickering M. EnderScope: a low-cost 3D printer-based scanning microscope for microplastic detection. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230214. [PMID: 38826048 DOI: 10.1098/rsta.2023.0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/21/2024] [Indexed: 06/04/2024]
Abstract
Low-cost and scalable technologies that allow people to measure microplastics in their local environment could facilitate a greater understanding of the global problem of marine microplastic pollution. A typical way to measure marine microplastic pollution involves imaging filtered seawater samples stained with a fluorescent dye to aid in the detection of microplastics. Although traditional fluorescence microscopy allows these particles to be manually counted and detected, this is a resource- and labour-intensive task. Here, we describe a novel, low-cost microscope for automated scanning and detection of microplastics in filtered seawater samples-the EnderScope. This microscope is based on the mechanics of a low-cost 3D printer (Creality Ender 3). The hotend of the printer is replaced with an optics module, allowing for the reliable and calibrated motion system of the 3D printer to be used for automated scanning over a large area (>20 × 20 cm). The EnderScope is capable of both reflected light and fluorescence imaging. In both configurations, we aimed to make the design as simple and cost-effective as possible, for example, by using low-cost LEDs for illumination and lighting gels as emission filters. We believe this tool is a cost-effective solution for microplastic measurement. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.
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Affiliation(s)
- Niamh Burke
- School of Medicine, University College Dublin , Dublin, Ireland
| | - Gesine Müller
- Multiscale Biology, Johann-Friedrich-Blumenbach Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen , Gottingen, Niedersachsen, Germany
| | - Vittorio Saggiomo
- Department of BioNanoTechnology, Wageningen University and Research , Wageningen, Gelderland, The Netherlands
| | | | - Jérôme Mutterer
- Institut de Biologie Moléculaire des Plantes, CNRS & Strasbourg University , Strasbourg, France
| | | | - Daniel Zakharov
- School of Medicine, University College Dublin , Dublin, Ireland
| | - Donal Healy
- School of Medicine, University College Dublin , Dublin, Ireland
| | - Emmanuel G Reynaud
- School of Biology & Environmental Science, University College Dublin , Dublin, Ireland
| | - Mark Pickering
- School of Medicine, University College Dublin , Dublin, Ireland
- UCD Centre for Biomedical Engineering, University College Dublin , Dublin, Ireland
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2
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Bowman R, Müllenbroich C, Diederich B, McConnell G, Faez S, Arancio J. Open, reproducible hardware for microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230112. [PMID: 38826046 DOI: 10.1098/rsta.2023.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 06/04/2024]
Affiliation(s)
- Richard Bowman
- School of Physics & Astronomy, University of Glasgow , Glasgow G12 8QQ, UK
| | | | - Benedict Diederich
- Leibniz Institute of Photonic Technology , Jena, Thuringia 07745, Germany
| | - Gail McConnell
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde , Glasgow G4 0RE, UK
| | - Sanli Faez
- Nanophotonics, Debye Institute for Nanomaterials Research, Utrecht University , Utrecht, The Netherlands
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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun 2024; 15:4941. [PMID: 38866781 PMCID: PMC11169475 DOI: 10.1038/s41467-024-49131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.
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Affiliation(s)
- Kohei Otomo
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery, University of Tokyo, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Nozawa
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
| | - Steven J Edwards
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yukihiko Sato
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuri Saito
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigehiro Yagishita
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Uchida
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Rin Yanai
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naruhiko Sahara
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiro Shiokawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Haruko Watanabe-Takano
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuka Haneda
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Miku Fujiwara
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takenobu Nii
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Takeshita
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Juan Marcelo Rosales Rocabado
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Yamada
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yumiko Oishi
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yinglan Cheng
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun-Ichiro Koga
- The Second Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kenichi Kimura
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Fuyuki Karube
- Lab of Histology and Cytology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyeree Kim
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinobu Hamada
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan.
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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4
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Le BT, Auer KM, Lopez DA, Shum JP, Suarsana B, Suh GYK, Hedde PN, Ahrar S. Orthogonal-view microscope for the biomechanics investigations of aquatic organisms. HARDWAREX 2024; 18:e00533. [PMID: 38711599 PMCID: PMC11070628 DOI: 10.1016/j.ohx.2024.e00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 05/08/2024]
Abstract
Microscopes are essential for the biomechanical and hydrodynamical investigation of small aquatic organisms. We report a prototype of a do-it-yourself microscope that enables the visualization of organisms from two orthogonal imaging planes - top and side views. Compared to conventional imaging systems, this approach provides a comprehensive visualization strategy of organisms, which could have complex shapes and morphologies. The microscope was constructed by combining custom 3D-printed parts and off-the-shelf components. The system is designed for modularity and reconfigurability. Open-source design files and build instructions are provided in this report. Additionally, proof-of-use experiments (particularly with Hydra) and other organisms that combine the imaging with an analysis pipeline were demonstrated to highlight the system's utility. Beyond the applications demonstrated, the system can be used or modified for various imaging applications.
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Affiliation(s)
- Brian T. Le
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Katherine M. Auer
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - David A. Lopez
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Justin P. Shum
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Brian Suarsana
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Ga-Young Kelly Suh
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Per Niklas Hedde
- Beckman Laser Institute and Medical Clinic, University of California Irvine, Irvine, CA 92612, USA
| | - Siavash Ahrar
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
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5
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Hümpfer N, Thielhorn R, Ewers H. Expanding boundaries - a cell biologist's guide to expansion microscopy. J Cell Sci 2024; 137:jcs260765. [PMID: 38629499 PMCID: PMC11058692 DOI: 10.1242/jcs.260765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Expansion microscopy (ExM) is a revolutionary novel approach to increase resolution in light microscopy. In contrast to super-resolution microscopy methods that rely on sophisticated technological advances, including novel instrumentation, ExM instead is entirely based on sample preparation. In ExM, labeled target molecules in fixed cells are anchored in a hydrogel, which is then physically enlarged by osmotic swelling. The isotropic swelling of the hydrogel pulls the labels apart from one another, and their relative organization can thus be resolved using conventional microscopes even if it was below the diffraction limit of light beforehand. As ExM can additionally benefit from the technical resolution enhancements achieved by super-resolution microscopy, it can reach into the nanometer range of resolution with an astoundingly low degree of error induced by distortion during the physical expansion process. Because the underlying chemistry is well understood and the technique is based on a relatively simple procedure, ExM is easily reproducible in non-expert laboratories and has quickly been adopted to address an ever-expanding spectrum of problems across the life sciences. In this Review, we provide an overview of this rapidly expanding new field, summarize the most important insights gained so far and attempt to offer an outlook on future developments.
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Affiliation(s)
- Nadja Hümpfer
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ria Thielhorn
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany
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6
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Last MGF, Voortman LM, Sharp TH. Building a super-resolution fluorescence cryomicroscope. Methods Cell Biol 2024; 187:205-222. [PMID: 38705625 DOI: 10.1016/bs.mcb.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Correlated super-resolution fluorescence microscopy and cryo-electron microscopy enables imaging with both high labeling specificity and high resolution. Naturally, combining two sophisticated imaging techniques within one workflow also introduces new requirements on hardware, such as the need for a super-resolution fluorescence capable microscope that can be used to image cryogenic samples. In this chapter, we describe the design and use of the "cryoscope"; a microscope designed for single-molecule localization microscopy (SMLM) of cryoEM samples that fits right into established cryoEM workflows. We demonstrate the results that can be achieved with our microscope by imaging fluorescently labeled vimentin, an intermediate filament, within U2OS cells grown on EM grids, and we provide detailed 3d models that encompass the entire design of the microscope.
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Affiliation(s)
- Mart G F Last
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lenard M Voortman
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas H Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands; School of Biochemistry, University of Bristol, Bristol, United Kingdom.
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7
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Zehrer AC, Martin-Villalba A, Diederich B, Ewers H. An open-source, high-resolution, automated fluorescence microscope. eLife 2024; 12:RP89826. [PMID: 38436658 PMCID: PMC10942636 DOI: 10.7554/elife.89826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user. Here, we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.
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Affiliation(s)
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research CenteHeidelbergGermany
| | | | - Helge Ewers
- Institut für Chemie und Biochemie, Freie Universität BerlinBerlinGermany
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8
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van den Wildenberg SMJL, Prevo B, Peterman EJG. A Brief Introduction to Single-Molecule Fluorescence Methods. Methods Mol Biol 2024; 2694:111-132. [PMID: 37824002 DOI: 10.1007/978-1-0716-3377-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
One of the most popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster resonance energy transfer and orientation measurements with fluorescence polarization.
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Affiliation(s)
- Siet M J L van den Wildenberg
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Université Clermont Auvergne, CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, Clermont-Ferrand, France
| | - Bram Prevo
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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9
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Prakash K. Correlative super-resolution microscopy with deep UV reactivation. J Microsc 2023. [PMID: 38145966 DOI: 10.1111/jmi.13258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/27/2023]
Abstract
Correlative super-resolution microscopy has the potential to accurately visualize and validate new biological structures past the diffraction limit. However, combining different super-resolution modalities, such as deterministic stimulated emission depletion (STED) and stochastic single-molecule localization microscopy (SMLM), is a challenging endeavour. For correlative STED and SMLM, the following poses a significant challenge: (1) the photobleaching of the fluorophores in STED; (2) the subsequent reactivation of the fluorophores for SMLM and (3) finding the right fluorochrome and imaging buffer for both imaging modalities. Here, we highlight how the deep ultraviolet (DBUE) wavelengths of the Mercury (Hg) arc lamp can help recover STED bleaching and allow for the reactivation of single molecules for SMLM imaging. We also show that Alexa Fluor 594 and the commercially available Prolong Diamond to be excellent fluorophores and imaging media for correlative STED and SMLM.
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Affiliation(s)
- Kirti Prakash
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
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10
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Martínez-Prat B, Arteaga O, Sagués F, Ignés-Mullol J. Multimodal fluorescence microscope with fast adaptive polarimetry. HARDWAREX 2023; 16:e00480. [PMID: 37817881 PMCID: PMC10560837 DOI: 10.1016/j.ohx.2023.e00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 08/02/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
Polarized light microscopy is a widely used technique to observe specimens that are optically anisotropic, or birefringent. It has a broad applicability in the study of minerals, soft materials such as polymers, complex fluids or liquid crystals, and organic tissues in biology and medicine. Most of these observations are qualitative in nature, as it is not obvious to quantify the spatial distribution of optical anisotropy of specimens. Moreover, existing commercial implementations for quantitative polarimetry are costly and slow in nature, precluding real time observation of dynamical processes. Here, we present a custom-made implementation of an optical microscope for quantitative polarimetry at the cost of a standard scientific polarizing microscope. The instrument allows to extract the local optical axis and birefringence of transparent materials with a frequency of several Hz. The instrument is built using off-the-shelf optomechanical components, which optimizes cost, availability, and modularity. An example of the latter is the fact that we combine the polarimetry measurements with simultaneous fluorescence microscopy, which results in a powerful multimodal instrument with broad potential applications.
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Affiliation(s)
- Berta Martínez-Prat
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
| | - Oriol Arteaga
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
| | - Francesc Sagués
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
| | - Jordi Ignés-Mullol
- Universitat de Barcelona and Institute of Nanoscience and Nanotechnology (IN2UB), Martíi Franquès 1, 08028, Barcelona, Spain
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11
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Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Imagining the future of optical microscopy: everything, everywhere, all at once. Commun Biol 2023; 6:1096. [PMID: 37898673 PMCID: PMC10613274 DOI: 10.1038/s42003-023-05468-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.
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Affiliation(s)
| | - Chad M Hobson
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA.
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12
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Hohlbein J. Open hardware in microscopy. HARDWAREX 2023; 15:e00473. [PMID: 37700785 PMCID: PMC10493255 DOI: 10.1016/j.ohx.2023.e00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The field of microscopy has been empowering humankind for many centuries by enabling the observation of objects that are otherwise too small to detect for the naked human eye. Microscopy techniques can be loosely divided into three main branches, namely photon-based optical microscopy, electron microscopy, and scanning probe microscopy with optical microscopy being the most prominent one. On the high-end level, optical microscopy nowadays enables nanometer resolution covering many scientific disciplines ranging from material sciences over the natural sciences and life sciences to the food sciences. On the lower-end level, simplified hardware and openly available description and blueprints have helped to make powerful microscopes widely available to interested scientists and researchers. For this special issue, we invited contributions from the community to share their latest ideas, designs, and research results on open-source hardware in microscopy. With this collection of articles, we hope to inspire the community to further increase the accessibility, interoperability, and reproducibility of microscopy. We further touch on the standardization of methodologies and devices including the use of computerized control of data acquisition and data analysis to achieve high quality and efficiency in research and development.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, the Netherlands
- Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, the Netherlands
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Niederauer C, Seynen M, Zomerdijk J, Kamp M, Ganzinger KA. The K2: Open-source simultaneous triple-color TIRF microscope for live-cell and single-molecule imaging. HARDWAREX 2023; 13:e00404. [PMID: 36923558 PMCID: PMC10009532 DOI: 10.1016/j.ohx.2023.e00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Imaging the dynamics and interactions of biomolecules at the single-molecule level in live cells and reconstituted systems has generated unprecedented knowledge about the biomolecular processes underlying many cellular functions. To achieve the speed and sensitivity needed to detect and follow individual molecules, these experiments typically require custom-built microscopes or custom modifications of commercial systems. The costs of such single-molecule microscopes, their technical complexity and the lack of open-source documentation on how to build custom setups therefore limit the accessibility of single-molecule imaging techniques. To advance the adaptation of dynamic single-molecule imaging by a wider community, we present the "K2": an open-source, simultaneous triple-color total internal reflection fluorescence (TIRF) microscope specifically designed for live-cell and single-molecule imaging. We explain our design considerations and provide step-by-step building instructions, parts list and full CAD models. The modular design of this TIRF microscope allows users to customize it to their scientific and financial needs, or to re-use parts of our design to improve the capabilities of their existing setups without necessarily having to build a full copy of the K2 microscope.
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Alsamsam MN, Kopūstas A, Jurevičiūtė M, Tutkus M. The miEye: Bench-top super-resolution microscope with cost-effective equipment. HARDWAREX 2022; 12:e00368. [PMID: 36248253 PMCID: PMC9556790 DOI: 10.1016/j.ohx.2022.e00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/23/2022] [Accepted: 10/02/2022] [Indexed: 06/01/2023]
Abstract
Commercial super-resolution (SR) imaging systems require a high budget, while current more affordable open source microscopy systems lack modularity and sometimes are too complex or lack reliability. We present miEye - a cost-effective microscope designed for high-resolution wide-field fluorescence imaging. The build is constructed using a CNC milled aluminum microscope body and commercially available optomechanics, with open-source Python-based microscope control, data visualization, and analysis software integration. The data acquisition software works robustly with commonly used industrial-grade complementary metal oxide semiconductor (iCMOS) cameras, performs IR beam back-reflection-based automatic focus stabilization, and allows for laser control via an Arduino-based laser relay. The open-source nature of the design is aimed to facilitate adaptation by the community. The build can be constructed for a cost of roughly 50 k €. It contains SM-fiber and MM-fiber excitation paths that are easy to interchange and an adaptable emission path. Also, it ensures <5 nm/min stability of the sample on all axes, and allows achieving <30 nm lateral resolution for dSTORM and DNA-PAINT single-molecule localization microscopy (SMLM) experiments. Thus it serves as a cost-effective and adaptable addition to the open source microscopy community and potentially will allow high-quality SR imaging even for limited-budget research groups.
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Affiliation(s)
- Mohammad Nour Alsamsam
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Aurimas Kopūstas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Meda Jurevičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marijonas Tutkus
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
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Prakash K, Diederich B, Heintzmann R, Schermelleh L. Super-resolution microscopy: a brief history and new avenues. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210110. [PMID: 35152764 PMCID: PMC8841785 DOI: 10.1098/rsta.2021.0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Super-resolution microscopy (SRM) is a fast-developing field that encompasses fluorescence imaging techniques with the capability to resolve objects below the classical diffraction limit of optical resolution. Acknowledged with the Nobel prize in 2014, numerous SRM methods have meanwhile evolved and are being widely applied in biomedical research, all with specific strengths and shortcomings. While some techniques are capable of nanometre-scale molecular resolution, others are geared towards volumetric three-dimensional multi-colour or fast live-cell imaging. In this editorial review, we pick on the latest trends in the field. We start with a brief historical overview of both conceptual and commercial developments. Next, we highlight important parameters for imaging successfully with a particular super-resolution modality. Finally, we discuss the importance of reproducibility and quality control and the significance of open-source tools in microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- Kirti Prakash
- Integrated Pathology Unit, Centre for Molecular Pathology, The Royal Marsden Trust and Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Benedict Diederich
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
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